BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3124792.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 708,372
number of mapped reads = 707,411 (99.86%)
number of supplementary alignments = 324,912 (45.87%)
number of secondary alignments = 0
number of mapped bases = 105,539,374 bp
number of sequenced bases = 105,513,464 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,027,205
duplication rate = 9.42%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.059
>>>>>>> ACTG content
number of A's = 31,754,106 bp (30.09%)
number of C's = 19,757,101 bp (18.72%)
number of T's = 33,694,258 bp (31.93%)
number of G's = 20,307,999 bp (19.25%)
number of N's = 0 bp (0%)
GC percentage = 37.97%
>>>>>>> Mismatches and indels
general error rate = 0.0073
number of mismatches = 765,122
number of insertions = 4,411
mapped reads with insertion percentage = 0.62%
number of deletions = 25,111
mapped reads with deletion percentage = 3.52%
homopolymer indels = 53.93%
>>>>>>> Coverage
mean coverageData = 0.0341X
std coverageData = 80.6448X
There is a 0.02% of reference with a coverageData >= 1X
There is a 0% of reference with a coverageData >= 2X
There is a 0% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 378836 0.0015198999243416127 1.0336687423394213
chr2 243199373 82731 3.401776862311236E-4 0.11750333456502275
chr3 198022430 48629 2.455731908753973E-4 0.1064614708568797
chr4 191154276 26412 1.3817111786712006E-4 0.011900661879530037
chr5 180915260 31411 1.7362272259399236E-4 0.01335877091477434
chr6 171115067 30013 1.7539659438639614E-4 0.03822552385133833
chr7 159138663 44478 2.79492105573364E-4 0.0940089021982504
chr8 146364022 65472 4.47323045003505E-4 0.1612207713413808
chr9 141213431 20991 1.4864733369448406E-4 0.01218393422964383
chr10 135534747 104478897 0.7708642935674643 385.412606859098
chr11 135006516 30907 2.2892969106765186E-4 0.05934475495490821
chr12 133851895 30000 2.2412831734657174E-4 0.016588757683134947
chr13 115169878 14970 1.299819037752215E-4 0.012827316665175536
chr14 107349540 32510 3.0284247142558786E-4 0.1807376641746294
chr15 102531392 23491 2.2911031969604002E-4 0.04214803876837879
chr16 90354753 18770 2.0773671972740604E-4 0.014844353296900691
chr17 81195210 17406 2.1437225176214214E-4 0.03201738720178762
chr18 78077248 59663 7.641534701632927E-4 0.29613034846481207
chr19 59128983 21253 3.5943456020544106E-4 0.08152291762759374
chr20 63025520 20713 3.2864465061137137E-4 0.058835236321179075
chr21 48129895 5959 1.2381078329798975E-4 0.013331650203844456
chr22 51304566 5863 1.1427832758589167E-4 0.010684934866977556
chrMT 16571 347 0.020940196729225757 0.14318416424370076
chrX 155270560 42980 2.768071423198319E-4 0.11490388502933736
chrY 59373566 6672 1.1237324030697431E-4 0.010943241044346198